EP0833902B1 - Spezifische oligonukleotide fuer hepatitis c-virus - Google Patents

Spezifische oligonukleotide fuer hepatitis c-virus Download PDF

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EP0833902B1
EP0833902B1 EP96920788A EP96920788A EP0833902B1 EP 0833902 B1 EP0833902 B1 EP 0833902B1 EP 96920788 A EP96920788 A EP 96920788A EP 96920788 A EP96920788 A EP 96920788A EP 0833902 B1 EP0833902 B1 EP 0833902B1
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oligonucleotide
seq
hcv
oligonucleotides
oligonucleotide according
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EP0833902A2 (de
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Bruce L. Frank
John Goodchild
Henry A. Hamlin, Jr.
Robert E. Kilkuskie
Noel A. Roberts
Peter C. Roberts
Debra M. Walther
Jia L. Wolfe
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Aceragen Inc
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Hybridon Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1131—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against viruses
    • C—CHEMISTRY; METALLURGY
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/706—Specific hybridization probes for hepatitis
    • C12Q1/707—Specific hybridization probes for hepatitis non-A, non-B Hepatitis, excluding hepatitis D
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/33—Chemical structure of the base
    • C12N2310/334—Modified C
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/346—Spatial arrangement of the modifications having a combination of backbone and sugar modifications

Definitions

  • This invention relates to hepatitis C virus. More particularly, this invention relates to oligonucleotides complementary to particular regions of hepatitis C virus nucleic acid and to methods of inhibiting the expression and replication of hepatitis C virus nucleic acid and protein using these oligonucleotides.
  • Hepatitis C virus is an enveloped, positive sense, single-stranded RNA virus which infects hepatocytes. HCV is the major cause of non-A, non-B, acute and chronic hepatitis (Weiner et al. (1990) Lancet 335:1-3), and has been associated with hepatocellular carcinoma (see, Dienstag et al. in Harrison's Principles of Internal Medicine, 13th Ed. (Isselbacher et al., eds.) McGraw-Hill, Inc. NY (1994) pp. 1458-1483).
  • the genome of HCV is a positive sense, single-stranded linear RNA of approximately 9,500 bases.
  • the organization of this genome is similar to pestiviruses and flaviviruses, with structural proteins at the 5' end and non-structural proteins at the 3' end (reviewed by Houghton et al. (1991) Hepatol. 14:381-388).
  • the viral RNA encodes a single polyprotein which is processed by viral and cellular proteases.
  • HCV also contains short 5' and 3' untranslated regions (UTR). The 5' UTR is the most highly conserved region of the virus (Bukh et al. (1992) Proc. Natl. Acad. Sci. (USA) 89:4942-4946).
  • HCV can be transmitted by transfusion and other percutaneous routes, such as self-injection with intravenous drugs.
  • this virus can be transmitted by occupational exposure to blood, and the likelihood of infection is increased in hemodialysis units (Boxag et al. in Harrison's Principles of Internal Medicine (13th Ed.) (Isselbacher et al., eds.) McGraw-Hill, Inc., NY (1994) pp. 1458-14843).
  • the risk of HCV infection is also increased in organ transplant recipients and in patients with AIDS; in all immunosuppressed groups, levels of anti-HCV antibodies may be undetectable, and a diagnosis may require testing for HCV RNA.
  • Chronic hepatitis C occurs in as many as 20 percent of renal transplant recipients. Five to 10 years after transplantation, complications of chronic liver disease account for increased morbidity and mortality (Felag et al., (ibid.).
  • chemotherapeutic agents have been developed which are capable of modulating cellular and foreign gene expression (see, Zamecnik et al. (1978) Proc. Natl. Acad. Sci. (USA) 75:280-284). These agents, called antisense oligonucleotides, bind to target single-stranded nucleic acid molecules according to the Watson-Crick rule or to double stranded nucleic acids by the Hoogsteen rule of base pairing, and in doing so, disrupt the function of the target by one of several mechanisms: by preventing the binding of factors required for normal transcription, splicing, or translation; by triggering the enzymatic destruction of mRNA by RNase H, or by destroying the target via reactive groups attached directly to the antisense oligonucleotide.
  • oligonucleotides have more recently been developed that have greater efficacy in inhibiting such viruses, pathogens and selective gene expression. Some of these oligonucleotides having modifications in their internucleotide linkages have been shown to be more effective than their unmodified counterparts. For example, Agrawal et al. (Proc. Natl. Acad. Sci. (USA) (1988) 85:7079-7083) teaches that oligonucleotide phosphorothioates and certain oligonucleotide phosphoramidates are more effective at inhibiting HIV-1 than conventional phosphodiester-linked oligodeoxynucleotides. Agrawal et al. (Proc. Natl. Acad. Sci. (USA) (1989) 86:7790-7794) discloses the advantage of oligonucleotide phosphorothioates in inhibiting HIV-1 in early and chronically infected cells.
  • chimeric oligonucleotides having more than one type of internucleotide linkage within the oligonucleotide have been developed.
  • Pederson et al. U.S. Patent Nos. 5,149,797 and 5,220,007 discloses chimeric oligonucleotides having an oligonucleotide phosphodiester or oligonucleotide phosphorothioate core sequence flanked by nucleotide methylphosphonates or phosphoramidates.
  • Agrawal et al. discloses hybrid oligonucleotides having regions of deoxyribonucleotides and 2'-O-methylribonucleotides.
  • Antisense oligonucleotides have been designed that are complementary to portions of the HCV genome. For example, oligonucleotides specific for various regions of the HCV genome have been developed (see, e.g., CA 2,104,649, WO 94/05813, WO 94/08002 and Wakita et al. (1994) J. Biol. Chem. 269:14205-14210). Unfortunately, no demonstration has been made in any reasonably predictive system that any of these oligonucleotides are capable of inhibiting the replication and expression of hepatitis C Virus.
  • oligonucleotides that are capable of inhibiting the replication and expression of hepatitis C virus whose uses are accompanied by a successful prognosis, and low or no cellular toxicity.
  • Antisense oligonucleotide technology provides a novel approach to the inhibition of HCV expression, and hence, to the treatment or prevention of chronic and acute hepatitis and of hepatocellular carcinoma (see generally, Agrawal (1992) Trends Biotech. 10:152; and Crooke (Proc. Am. Ass. Cancer Res. Ann. Meeting (1995) 36:655).
  • antisense oligonucleotides are able to inhibit splicing and translation of RNA, and replication of genomic RNA. In this way, antisense oligonucleotides are able to inhibit protein expression.
  • the present invention provides oligonucleotides useful for inhibiting the replication of HCV or the expression of HCV genomic or messenger RNA or protein in a cell, and for treating HCV infection.
  • oligonucleotide sequence that is complementary to genomic or mRNA is intended to mean an oligonucleotide that binds to the nucleic acid sequence under physiological conditions, e.g., by Watson-Crick base pairing (interaction between oligonucleotide and single-stranded nucleic acid) or by Hoogsteen base pairing (interaction between oligonucleotide and double-stranded nucleic acid) or by any other means including in the case of a oligonucleotide binding to RNA, causing pseudoknot formation. Binding by Watson-Crick or Hoogsteen base pairing under physiological conditions is measured as a practical matter by observing interference with the function of the nucleic acid sequence.
  • the present invention provides a synthetic oligonucleotide complementary to a sequence consisting of two non-contiguous regions of an HCV messenger or genomic RNA.
  • Non-contiguous oligonucleotides are targeted to at least two regions of the HCV genomic RNA or mRNA which are not contiguous in a linear sense but, which may be next to each other in three dimensional space due to the secondary structure or conformation of the target molecule (FIGS. 2A and 2B).
  • one or both portions of the "non-contiguous" oligonucleotide is complementary to the 5' untranslated region.
  • One portion of some non-contiguous oligonucleotides includes the same 12 bases (bases 100-111) designated the "anchor" region.
  • the other portion of such non-contiguous oligonucleotides is variable, containing 6 to 12 bases within, e.g., bases 315-340 of HCV nucleic acid.
  • one portion which is complementary to the 5' untranslated region comprises the sequence GGGGUCCUGGAG (SEQ ID NO:47), and the other portion is complementary to a 5' region of the RNA encoding the HCV C protein.
  • Other non-contiguous oligonucleotides of the invention may be targeted to other non-contiguous regions of HCV nucleic acid.
  • the portion which is complementary to the 5' untranslated region and which functions as an anchor comprises the sequence CAACACUACUCG (bases 243-254).
  • the non-contiguous oligonucleotide has about 18 to about 24 nucleotides in length.
  • the non-contiguous oligonucleotide which is complementary to two non-contiguous regions comprises one of the sequences as set forth in the Sequence Listing as SEQ ID NO:38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, and 67, or as set forth in Table 1C as SEQ ID NO: 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147.
  • an oligonucleotide may bind to three non-continuous regions. These oligonucleotides are called tripartite non-contiguous oligonucleotides (see for example, Table 1D). The tripartite oligonucleotides are developed as described herein for non-contiguous oligonucleotides using non-continuous oligonucleotides (as described herein) as a 2' OMe RNA anchor with a short semi-randomized DNA sequence attached.
  • RNAase H RNAase H
  • the specific tripartite oligonucleotide of the invention may be designed.
  • the invention provides corresponding oligonucleotides as set forth in Table 1D under SEQ ID NOS: 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158.
  • the oligonucleotides of the invention are modified.
  • these modifications include at least one internucleotide linkage selected from the group consisting of alkylphosphonate, phosphorothioate, phosphorpdithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester including combinations of such linkages, as in a chimeric oligonucleotide.
  • an oligonucleotide of the invention comprises at least one phosphorothioate internucleotide linkage.
  • the oligonucleotide comprises at least one or at least two inosine residues at any position in the oligonucleotide. In another embodiment, the oligonucleotide contains one or more 5-methyl-2'-deoxycytidine residues instead of the 2'deoxycytidine.
  • the oligonucleotides of the invention may also include at least one deoxyribonucleotide, at least one ribonucleotide, or a combination thereof, as in a hybrid oligonucleotide.
  • An oligonucleotide containing at least one 2'-O-methyl ribonucleotide is one embodiment of the invention.
  • the oligonucleotide consists of deoxyribonucleotides only.
  • the oligonucleotides may be further modified as outlined below.
  • the oligonucleotides of the present invention are for use as therapeutically active compounds, especially for use in the control or prevention of hepatitis C virus infection.
  • the invention provides a pharmaceutical composition comprising at least one non-contiguous HCV-specific oligonucleotide of the invention as described above and below, and in some embodiments, this composition includes at least two different oligonucleotides (i.e., having a different nucleotide sequence, length, and/or modification(s)).
  • the pharmaceutical composition of some embodiments is a physical mixture of at least two, and preferably, many oligonucleotides with the same or different sequences, modifications, and/or lengths.
  • this pharmaceutical formulation also includes a physiologically or pharmaceutically acceptable carrier.
  • a therapeutic amount of a pharmaceutical composition containing HCV-specific synthetic oligonucleotides is administered to the cell for inhibiting hepatitis C virus replication or of treating hepatitis C virus infection.
  • the HCV-specific oligonucleotides are the non-contiguous oligonucleotides of the invention.
  • the use includes administering at least one non-contiguous oligonucleotide, or at least two non-contiguous oligonucleotides, having a sequence set forth in Table 2 or in the Sequence Listing as SEQ ID NO: 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, and 67, or as set forth in Tables 1C-1E as SEQ ID NOS: 134-158 and 166-170, or a combination thereof.
  • the oligonucleotides may also be used in modified form.
  • oligonucleotide(s) of the invention at least one, and preferably two or more identical or different oligonucleotides may be administered simultaneously or sequentially as a single treatment episode in the form of separate pharmaceutical compositions.
  • the invention provides a method of detecting the presence of HCV in a sample, such as a solution or biological sample.
  • a sample such as a solution or biological sample.
  • the sample is contacted with a synthetic oligonucleotide of the invention. Hybridization of the oligonucleotide to the HCV nucleic acid is then detected if the HPV is present in the sample.
  • kits for detecting HCV in a sample include at least one synthetic, non-contiguous oligonucleotide of the invention, which may have the same or different nucleotide sequence, length, and/or modification(s), and means for detecting the oligonucleotide hybridized with the nucleic acid.
  • oligonucleotides of the invention are composed of deoxyribonucleotides, ribonucleotides, 2-O-methylribonucleotides, or any combination thereof, with the 5' end of one nucleotide and the 3' end of another nucleotide being covalently linked.
  • These oligonucleotides are preferably 12 to 50 nucleotides long, with 20 to 30mers being the most common.
  • oligonucleotides can be prepared by art recognized methods.
  • nucleotides can be covalently linked using art-recognized techniques such as phosphoramidite, H-phosphonate chemistry, or methylphosphonamidate chemistry (see, e.g., Goodchild (1990) Chem. Rev. 90:543-584; Uhlmann et al. (1990) Chem. Rev. 90:543-584; Caruthers et al. (1987) Meth. Enzymol. 154:287-313; U.S. Patent 5,149,798) which can be carried out manually or by an automated synthesizer and then processed (reviewed in Agrawal et al. (1992) Trends Biotechnol. 10:152-158).
  • oligonucleotides of the invention may also be modified in a number of ways without compromising their ability to hybridize to HCV genomic or messenger RNA.
  • the oligonucleotides may contain other than phosphodiester internucleotide linkages between the 5' end of one nucleotide and the 3' end of another nucleotide in which other linkage, the 5' nucleotide phosphate has been replaced with any number of chemical groups, such as a phosphorothioate.
  • Oligonucleotides with phosphorothioate linkages can be prepared using methods well known in the field such as phosphoramidite (see, e.g., Agrawal et al. (1988) Proc. Natl.
  • US Patent No. 5,149,797 describes traditional chimeric oligonucleotides having a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions.
  • Other chimerics are "inverted" chimeric oligonucleotides comprising one or more nonionic oligonucleotide regions (e.g alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkage) flanked by one or more regions of oligonucleotide phosphorothioates.
  • Chimerics and inverted chimerics may be synthesized as discussed in the Examples for methyl phosphonate containing oligonucleotides. These "chimerics” and “inverted chimeric” oligonucleotides are a preferred embodiment for the modification of the oligonucleotides of the present invention.
  • oligonucleotides with modified internucleotide linkages can be prepared according to known methods (see, e.g., Goodchild (1990) Bioconjugate Chem. 2:165-187; Agrawal et al. (1988) Proc. Natl. Acad, Sci. (USA) 85:7079-7083; Uhlmann et al. (1990) Chem. Rev. 90:534-583; and Agrawal et al. (1992) Trends Biotechnol. 10:152-158).
  • Oligonucleotides which are self-stabilized are also considered to be modified oligonucleotides useful in the methods of the invention (Tang et al. (1993) Nucleic Acids Res 20; 2729-2735). These oligonucleotides comprise two regions: a target hybridizing region; and a self-complementary region having an oligonucleotide sequence complementary to a nucleic acid sequence that is within the self-stabilized oligonucleotide. These oligonucleotides form looped structures which are believed to stabilize the 3' end against exonuclease attack while still allowing hybridization to the target.
  • modifications to sugars include modifications to the 2' position of the ribose moiety which include but are not limited to 2'-O-substituted with an -O- lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an -O-aryl, or allyl group having 2-6 carbon atoms wherein such -O-alkyl, aryl or allyl group may be unsubstituted or may be substituted (e.g., with halo, hydroxy, trifluoromethyl, cyano, nitro acyl acyloxy, alkoxy, carboxy, carbalkoxyl, or amino groups), or with an amino, or halo group.
  • PCT Publication No. WO 94/02498 discloses traditional hybrid oligonucleotides having regions of 2'-O-substituted ribonucleotides flanking a DNA core region.
  • hybrid oligonucleotide which includes an oligonucleotide comprising a 2'-O-substituted (or 2' OH, unsubstituted) RNA region which is interposed between two oligodeoxyribonucleotides regions, a structure that is inverted relative to the "traditional" hybrid oligonucleotides.
  • Hybrid and inverted hybrid oligonucleotides may be synthesized as described in the Examples for oligonucleotides containing 2'-0-methyl RNA.
  • the hybrid and inverted hybrid oligonucleotides of the invention are particularly preferred due to the enhanced stability and activity over time in the presence of serum.
  • the hybrid or inverted hybrid may comprise at least one n-butyl phosphoramidate or methylphosphonate linkage.
  • the ribonucleotide is a 2-0-methyl ribonucleotide.
  • the oligoriucleotide comprises at least one, preferably one to five 2-0-methyl ribonucleotides at the 3' end of the oligonucleotide.
  • the oligonucleotide may further comprise at least one, preferably one to five 2-0-methyl ribonucleotides at the 5'-end.
  • oligonucleotide structures of the invention include the so-called dumbell and nicked dumbell structures. Ashly and Kushlan (Biochem. (1991) 30:2927-2933) describe the synthesis of oligonucleotide dumbells including nicked dumbells.
  • a dumbell is a double-helical stem closed off by two hairpin loops.
  • the antisense activity of nicked dumbells is discussed by Yamakawa et al. (Nucleosides and Nucleotides (1996) 15:519-529).
  • These oligonucleotides structures are believed to have beneficial properties similar to those of the self-stabilized oligonucleotides described above.
  • the present invention relates to non-contiguous multiplex oligonucleotides which are designed to target a polypurine or polypyrimidine sequence by a combination of duplex and triplex formation.
  • the multiplex oligonucleotide of the invention may be branched by adding linkers for supporting branched moieties as is known in the art.
  • the multiplex oligonucleotides of the invention need not be continuous and may bind to two or more proximal sites as described herein for non-contiguous oligonucleotides.
  • Preferred non-contiguous multiplex oligonucleotides of the invention having SEQ ID NOS: 166-170 are shown in Table 1E. These oligonucleotides target the double strand RNA stem at -217 to -209 and the adjacent polypyrimidine sequence between -218 and -222. The hybridization of an antisense sequence to the single stranded polypyrimidine target creates a polypurine-polypyrimidine , duplex that can be targeted by a triplex motif to increase the oligonucleotide binding strength. These oligonucleotides therefore provide a portion of the triplex target by duplex formation with the RNA as well as the third strand of the triple helix.
  • the multiplex oligonucleotides as designed contain an RNase H active portion for irreversible inactivation of the target RNA.
  • the asymmetric branching amidite (Y) (Clone Tech. Palo Alto, California) is incorporated during solid phase synthesis and hydrolyzed with hydrazine monohydrate according to the manufacturer's instructions. The branching strand is added subsequently by the same solid phase approach.
  • modifications include those which are internal or are at the end(s) of the oligonucleotide molecule and include additions to the molecule of the internucleoside phosphate linkages, such as cholesteryl, cholesterol or diamine compounds with varying numbers of carbon residues between the two amino groups, and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the viral genome.
  • cholesteryl cholesterol or diamine compounds with varying numbers of carbon residues between the two amino groups
  • terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the viral genome.
  • modified oligonucleotides include oligonucleotides with a modified base and/or sugar such as arabinose instead of ribose, or a 3', 5'-substituted oligonucleotide having a sugar which, at one or both its 3' and 5' positions is attached to a chemical group other than a hydroxyl or phosphate group (at its 3' or 5' position).
  • oligonucleotides capped with ribose at the 3' end of the oligonucleotide may be subjected to NaIO 4 oxidation/reductive amination.
  • Amination may include but is not limited to the following moieties, spermine, spermidine, Tris(2-aminoethyl) amine (TAEA), DOPE, long chain alkyl amines, crownethers, coenzyme A, NAD, sugars, peptides, dendrimers.
  • At least one cytosine base may be modified by methylation as is known in the art, e.g., 5-methylated deoxycytosine (5-Me-dC) (see Table 1B).
  • methylation may be desirable, for example, to reduce immune stimulation by the oligonucleotide if necessary.
  • modified oligonucleotides are capped with a nuclease resistance-conferring bulky substituent at their 3' and/or 5' end(s), or have a substitution in one or both nonbridging oxygens per nucleotide.
  • Such modifications can be at some or all of the internucleoside linkages, as well as at either or both ends of the oligonucleotide and/or in the interior of the molecule (reviewed in Agrawal et al. (1992) Trends Biotechnol. 10:152-158), some non-limiting examples of capped species include 3' O-methyl, 5' O-methyl, 2' O-methyl, and any combination thereof, as shown in Table 1B
  • an oligonucleotide of the invention is capable of successfully binding to its target.
  • One assay is an RNase H assay (Frank et al. (1993) Proc. Int. Conf. Nucleic Acid Med. Applns. 1:4.14(abstract)) which is useful when a region of at least four contiguous nucleotides of the oligonucleotide is DNA and the target is RNA. Binding of the DNA portion of the oligonucleotide (ODN) to the RNA target is identified by cleavage at that site by RNase H, as shown schematically in FIG. 3.
  • HCV mRNA three regions of HCV mRNA were investigated as RNase H sensitive areas, and were shown to be susceptible to hybridization by members of a degenerate 20mer library, Regions A, B, and C.
  • the assay was performed with several oligodeoxynucleotide phosphorothioate 20mers targeted to these three regions and present at a concentration of 100 nM.
  • the assays relating to contiguous oligonucleotides are only comparative examples. Contiguous oligonucleotides set forth in Table 1F are only for illustrative purposes.
  • Region A (or site 2) (located around the start codon) shows two peaks of activity in the RNase H cleavage assay with oligonucleotides targeted to -12 to +8 and +1 to +20 (FIG. 4B).
  • Region B (or site 1) (located upstream at approximately bases 210-260) shows a single peak of activity that corresponds to an oligonucleotide 20mer from -237 to -218 (FIG. 4A).
  • Region C (located upstream at bases 50-80) shows one peak of activity in this assay, for oligonucleotides targeted to -69 to -88 (FIG. 4C).
  • a sequence in Region B was selected as the anchor for a semirandom oligonucleotide probe (SOP).
  • SOP has a defined 2'-OMe RNA "anchor" sequence complementary to bases -219 to -230 in Region B and a six base random DNA "tail" on either its 5' or 3' end.
  • the 2'-OMe RNA portion cannot activate RNase H cleavage and a six base random DNA library without the anchor does not activate RNase H cleavage of the transcript under these conditions.
  • RNase H cleavage only occurs by the anchor-facilitated binding of the six-base DNA tail to the target.
  • These semirandom oligonucleotides efficiently activate RNase H cleavage at several sites, including near the anchor, near the start codon (Region A) and within the coding region of the mRNA.
  • Region A was targeted with non-contiguous oligonucleotide probes (NOPs).
  • NOPs non-contiguous oligonucleotide probes
  • a series of NOPs were prepared that were able to bridge between Regions A and B. Maintaining the 2'-OMe anchor of the semirandomers (-219 to -230) allowed the sequence of the six base tail and the site of attachment to the anchor to be varied to find the best bridging sequence. The results of this experiment suggests that attaching the tail to different ends of the anchor gives a different optimal sequence, as shown by the different peaks of activity with RNase H. (FIG. 5).
  • the chemistry of the anchor of one NOP was modified to examine its effect on the binding strength of the tail. As shown in FIG. 6, modification of the 2'-OMe phosphodiester (PO) anchor to 2'-OMe phosphorothioate (PS) and DNA PS effected the cleavage efficiency of the tail. Cleavage paralleled the expected binding strength of the anchor, 2'-OMe PO > 2'-OMe PS > DNA PS.
  • PO 2'-OMe phosphodiester
  • PS 2'-OMe phosphorothioate
  • DNA PS DNA PS
  • oligonucleotide sequences were evaluated as antisense inhibitors of HCV 5, UTR-dependent protein expression (FIG. 1). Some of these oligonucleotides had different chemical backbone modifications. These oligonucleotides were evaluated in three cellular assay systems: (1) inhibition of HCV luciferase (HCVLUC) fusion protein expression in stably transfected cells; (2) inhibition of HCV RNA expression in stably transfected cells; and (3) inhibition of HCV protein expression in Semliki Forest virus/HCV recombinant virus infected cells. They were also evaluated in RNase H cleavage.
  • HCVLUC HCV luciferase
  • the 5' UTR region of HCV containing the ATG start site was cloned 5' to the open reading frame of firefly luciferase (FIG. 8). Transcription of this HCV-luciferase gene fusion is stimulated in mammalian cells by a strong constitutive CMV promoter. Translation of the fusion gene is initiated at the HCV ATG which replaced the native luciferase ATG, and produces a protein which contains the first three amino acids of the viral protein and 648 amino acids of luciferase.
  • Expression of this enzyme in mammalian cells can be quantified easily in a luminometer by addition of luciferin substrate and ATP cofactor to the lysed cells.
  • Antisense oligonucleotides when added to mammalian cells expressing this fusion construct, will reduce luciferase activity if these compounds target sequences within the 5' UTR of HCV and/or luciferase.
  • FIG. 9 shows a dose response for inhibition by oligonucleotide HCV1 (SEQ ID NO:28).
  • This oligonucleotide is antisense to HCV sequences 244 to 263 (-86 to -67 relative to the start of translation for HCV) (see FIG. 1 and Table 1).
  • HCV1 inhibited luciferase by more than 50% at 1 and 0.2 ⁇ M relative to cells treated without oligonucleotide. No inhibition was observed at 0.04 and 0.008 ⁇ M.
  • oligonucleotides targeted at different sequences in the 5' UTR were evaluated in this assay system (FIG. 1). Dose response curves (1 ⁇ M to 0.008 ⁇ M) were developed for all oligonucleotide sequences. In all oligonucleotides tested, 0.2 ⁇ M was the lowest concentration which showed significant luciferase inhibition. A summary of the inhibition at 0.2 ⁇ M is shown in FIG. 10. Not all oligonucleotides targeted against HCV 5' UTR sequences inhibited luciferase expression. More active oligonucleotides (for example, HCV1 and HCV3) had percent control values less than or equal to 50 percent in these experiments.
  • oligonucleotides for example, HCV37 (SEQ ID NO:69) and HCV14 (SEQ ID NO:70) had percent control values greater than 100 percent.
  • the most active oligonucleotides were HCV1, HCV3, and HCV28. All are targeted in the same region, HCV sequences 240 to 290.
  • a second region, HCV sequences 80 to 140, also was complementary to oligonucleotides that inhibited luciferase.
  • oligonucleotides evaluated in this assay were designed to bind to HCV sequences. Since HCVLUC created a fusion between HCV and luciferase sequences 9 bases into the coding sequence, oligonucleotides HCV8, HCV10, and HCV19-23 all had greater than 4 mismatches with the HCVLUC sequence. None of these oligonucleotides inhibited luciferase expression. These results also confirm that sequence specific interaction with the target was required for luciferase inhibition.
  • Non-contiguous oligonucleotides were also evaluated in this assay. Oligonucleotides HCV53 (SEQ ID NO:39), HCV112 (SEQ ID NO:64), and HCV125 (SEQ ID NO:66), were tested and found to inhibit HCVLUC by greater than or equal to 50% at 1 ⁇ M. In addition to the anchor region, HCV53 targeted bases 324 to 329; HCV112 targeted sequences 324 to 335. This region may be particularly important for inhibition in these non-contiguous oligonucleotides.
  • Oligonucleotides targeted at the HCV 5' untranslated region inhibited translation of a protein which was fused to the 5' untranslated region sequence.
  • a longer HCV construct was also evaluated.
  • This construct contained HCV sequences 52-1417, which encoded the C and E1 protein of HCV.
  • the HCV construct was used to evaluate antisense oligonucleotide interaction with a larger HCV RNA. It was believed that this RNA secondary structure might resemble the HCV viral RNA more closely than the HCVLUC RNA. RNA levels were measured after oligonucleotide treatment to directly evaluate the interaction of oligos with their target.
  • FIGS. 11A and 11B Treatment of HepG2 HCV (52-1417) cells with antisense oligonucleotide decreased the amount of HCV specific RNA, as shown in FIGS. 11A and 11B.
  • HepG2 cells which were not transfected with the HCV construct do not produce a specific, HCV related band with probe 1 (FIG. 11A). Similar experiments were conducted to show the specificity of probe 2 (FIG. 11B).
  • FIG. 11A and 11B show that HCV1 and HCV3 decreased HCV RNA in HCV (52-1417) cells. The amounts of full length HCV RNA were quantitated on the phosphorimager and compared to untreated cells (Table 3).
  • Probe 1 Probe 2 HCV1 (SEQ ID NO:28) 1.0 0 21 0.2 47 69 0.04 92 77 HCV3 (SEQ ID NO:35) 1.0 38 60 0.2 54 72 0.04 55 63 R20 (random) 1.0 316 254 0.2 454 471 0.04 126 125
  • HCV1 and HCV3 decreased RNA levels by greater than 40% at concentrations greater than or equal to 0.2 ⁇ M.
  • Random oligonucleotide increased HCV RNA by greater than 3 fold at concentrations greater than or equal to 0.2 ⁇ M.
  • HCV1 and HCV3 were targeted to sequences 6-25 and 21-40 bases from the 5' end of the RNA/probe hybrid. Also, HCV1 and HCV3 are targeted to HCV RNA sequences 15 bases apart. The lower molecular weight bands detected on the gel were consistently about 15 bases apart.
  • oligonucleotide specific RNA cleavage in cells was compared to in vitro cleavage of RNA/oligonucleotide hybrids by RNase H.
  • HCV RNA was transcribed in vitro witl. T7 RNA polymerase and incubated with specific oligonucleotides and RNase H. RNA was then precipitated, and ribonuclease protection assays performed. Assays were performed as described above except that 0.1 ng in vitro transcribed RNA was used in the ribonuclease protection assay. Molecular weights of bands were determined by comparison to RNA standards.
  • HCV1 produced bands 90-95 bases less than full length RNA
  • HCV3 produced bands 70-80 bases less than full length RNA
  • probe 2 FIG. 11C
  • products were 13-17 bases less than full length for HCV1, 20-30 bases less than full length for HCV3.
  • SFV/HCV recombinant virus was prepared as a model system for measuring HCV protein production after virus infection.
  • pSFV1/HCV (containing HCV sequence 1-2545) was prepared from a plasmid (Hoffman-Roche, Basel, Switzerland) and pSFV1 (Gibco/BRL, Gaithersburg, MD).
  • RNA transcribed from pSFV1/HCV produces SFV replicase proteins which replicate the input RNA and produce multiple copies of subgenomic mRNA.
  • the subgenomic RNA contains the 5' end of HCV RNA plus approximately 50 bases derived from the pSFV1 vector. This model has the advantages of cytoplasmic replication and a 5' end very similar to authentic HCV.
  • Recombinant SFV/HCV infected three cell types HepG2; CHO; and BHK21. Infection was monitored by HCV C protein production. Cells were infected for 1 hour, inoculum was removed, and cells were cultured overnight. Cells were lysed and protein separated on a 13.3% polyacrylamide/SDS gel. Proteins were electroblotted onto nitrocellulose and detected by Western blot using rabbit anti-HCV C protein antiserum. Protein was detected after infection with a 1/750 virus dilution in HepG2 and CHO cells and 1/3750 virus dilution in BHK21 cells. Antisense experiments were conducted in HepG2 cells using a 1/100 virus dilution.
  • HCV C protein was decreased in the presence of HCV1. The inhibition was 50% at 2 ⁇ M and 0.4 ⁇ M HCV1. No consistent decrease was detected in randomer treated cells.
  • HCV3 inhibited C protein production by about 60 to 70% at 0.4 ⁇ M
  • HCV8 inhibited C protein production by about 40% at 2 ⁇ M and 0.4 ⁇ M.
  • the SFV/HCV recombinant provided a model system for HCV replication, and in a sequence specific inhibition of HCV protein expression was measured.
  • modified oligonucleotides were evaluated as luciferase inhibitors in HepG2 HCVLUC cells. Experiments were conducted with phosphorothioate oligodeoxynucleotides and with oligonucleotides having additional backbone modifications (chimeric and hybrid). In addition, the effects of oligonucleotide length on activity of modified backbones were also evaluated. The results of these experiments are shown in Table 5 below.
  • Hybrid oligonucleotides containing five 2'OMe phosphodiester residues at the 3' end (EG4-29) or five 2'OMe phosphodiester residues at both ends (EG4-65) were less active than their phosphorothioate counterparts. This suggests that phosphorothioate linkages are required for maximum activity.
  • Chimeric oligonucleotides can be prepared which contained phosphoramidate or methylphosphonate linkages in addition to phosphorothioate linkages. All sequences were based on HCV36 (SEQ ID NO:68) or HCV25 (SEQ ID NO:26). The results of luciferase inhibition studies using oligonucleotides having phosphorothioate and methylphosphonate linkages are shown below in Table 6. Compound Sequence SEQID No.
  • antisense activity as measured by luciferase inhibition, was retained in molecules with several backbone modifications: (1) oligonucleotides with phosphorothioate internucleotide linkages, (2) hybrids with DNA phosphorothioate internucleotide linkages and 2'-O-methyl RNA; (3) chimeric oligonucleotides having phosphorothioate and methylphosphonate internucleotide linkages.
  • Chimeric oligonucleotides having phosphorothioate and PNBu internucleotide linkages and chimeric oligonucleotides having phosphorothioate and PNH(CH 2 ) 6 NH 3+ internucleotide linkages should also be effective.
  • Antisense activity appeared to require phosphorothioate rather than phosphodiester backbones; longer chain lengths with chimeric oligonucleotides (that hybridize less strongly); and the ability to activate ribonuclease H.
  • the synthetic antisense oligonucleotides of the invention in the form of a therapeutic composition or formulation are useful in inhibiting HCV replication in a cell, and in treating hepatitis C viral infections and resulting conditions in an animal, such as chronic and acute hepatitis, hepatocellular carcinoma. They may be used on or as part of a pharmaceutical composition when combined with a physiologically and/or pharmaceutically acceptable carrier. The characteristics of the carrier will depend on the route of administration.
  • a composition may contain, in addition to the synthetic oligonucleotide and carrier, diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art.
  • the pharmaceutical composition of the invention may also contain other active factors and/or agents which enhance inhibition of HCV expression.
  • active factors and/or agents which enhance inhibition of HCV expression.
  • the pharmaceutical composition of the invention may further contain other chemotherapeutic drugs.
  • additional factors and/or agents may be included in the pharmaceutical composition to produce a synergistic effect with the synthetic oligonucleotide of the invention, or to minimize side-effects caused by the synthetic oligonucleotide of the invention.
  • the synthetic oligonucleotide of the invention may be included in formulations of a particular anti-HCV or anti-cancer factor and/or agent to minimize side effects of the anti-HCV factor and/or agent.
  • the pharmaceutical composition of the invention may be in the form of a liposome in which the synthetic oligonucleotides of the invention is combined, in addition to other pharmaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers which are in aqueous solution.
  • Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent No.
  • the pharmaceutical composition of the invention may further include compounds such as cyclodextrins and the like which enhance delivery of oligonucleotides into cells , or such as slow release polymers.
  • the term "therapeutically effective amount” or “therapeutic amount” means the total amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful patient benefit, i.e., reduction in chronic or acute hepatitis or hepatocellular carcinoma.
  • a meaningful patient benefit i.e., reduction in chronic or acute hepatitis or hepatocellular carcinoma.
  • the term refers to that ingredient alone.
  • the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
  • a therapeutically effective amount of one or more of the synthetic oligonucleotides of the invention is administered to a subject afflicted with an HCV-associated disease.
  • the synthetic oligonucleotide of the invention may be administered in accordance with the method of the invention either alone of in combination with other known therapies for the HCV-associated disease.
  • the synthetic oligonucleotide of the invention may be administered either simultaneously with the other treatment(s), or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering the synthetic oligonucleotide of the invention in combination with the other therapy.
  • Administration of the synthetic oligonucleotide of the invention used in the pharmaceutical composition or to practice the method of treating an animal can be carried out in a variety of conventional ways, such as intraocular, oral ingestion, inhalation, or cutaneous, subcutaneous, intramuscular, or intravenous injection.
  • the synthetic oligonucleotide When a therapeutically effective amount of synthetic oligonucleotide of the invention is administered orally, the synthetic oligonucleotide will be in the form of a tablet, capsule, powder, solution or elixir.
  • the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant.
  • the tablet, capsule, and powder contain from about 5 to 95% synthetic oligonucleotide and preferably from about 25 to 90% synthetic oligonucleotide.
  • a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, sesame oil, or synthetic oils may be added.
  • the liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol.
  • the pharmaceutical composition When administered in liquid form, contains from about 0.5 to 90% by weight of the synthetic oligonucleotide and preferably from about 1 to 50% synthetic oligonucleotide.
  • the synthetic oligonucleotide of the invention When a therapeutically effective amount of synthetic oligonucleotide of the invention is administered by intravenous, cutaneous or subcutaneous injection, the synthetic oligonucleotide will be in the form of a pyrogen-free, parenterally acceptable aqueous solution.
  • parenterally acceptable solutions having due regard to pH, isotonicity, stability, and the like, is within the skill in the art.
  • a preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to the synthetic oligonucleotide, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art.
  • an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art.
  • the pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art.
  • the amount of synthetic oligonucleotide in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone. Ultimately, the attending physician will decide the amount of synthetic oligonucleotide with which to treat each individual patient. Initially, the attending physician will administer low doses of the synthetic oligonucleotide and observe the patient's response. Larger doses of synthetic oligonucleotide may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should contain about 1.0 ng to about 2.5 mg of synthetic oligonucleotide per kg body weight.
  • the duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual patient. It is contemplated that the duration of each application of the synthetic oligonucleotide will be in the range of 12 to 24 hours of continuous intravenous administration. Ultimately the attending physician will decide on the appropriate duration of intravenous therapy using the pharmaceutical composition of the present invention.
  • kits for inhibiting hepatitis C virus replication and infection in a cell includes a synthetic oligonucleotide specific for HCV genomic or messenger RNA, such as those described herein.
  • the kit may include at least one of the non-contiguous oligonucleotides having SEQ ID NO: 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65 66, and 67 and/or those oligonucleotides having SEQ ID NOS: 134-158 and 166-170 and listed in Tables 1C-1E.
  • oligonucleotides may have modified backbones, such as those described above, and may be RNA/DNA hybrids containing, for example, at least one 2'-O-methyl.
  • the kit of the invention may optionally include buffers, cell or tissue preparation reagents, cell or tissue preparation tools, vials, and the like.
  • the invention provides a method of detecting the presence of HCV in a sample, such as a solution or biological sample.
  • a sample such as a solution or biological sample.
  • the sample is contacted with a synthetic oligonucleotide of the invention. Hybridization of the oligonucleotide to the HCV nucleic acid is then detected if the- HCV is present in the sample.
  • kits for detecting HCV in a sample include a non-contiguous synthetic oligonucleotide of the invention, and means for detecting the oligonucleotide hybridized with the nucleic acid.
  • Oligonucleotides were synthesized using standard phosphoramidite chemistry (Beaucage (1993) Meth. Mol. Biol. 20:33-61; Uhlmann et al. (1990) Chem. Rev, 90:543-584) on either an ABI 394 DNA/RNA synthesizer (Perkin-Elmer, Foster City, CA), a Pharmacia Gene Assembler Plus (Pharmacia, Uppsala, Sweden) or a Gene Assembler Special (Pharmacia, Uppsala, Sweden) using the manufacturers standard protocols and custom methods.
  • the custom methods served to increase the coupling time from 1.5 min to 12 min for the 2'-OMe RNA amidites.
  • the Pharmacia synthesizers required additional drying of the amidites, activating reagent and acetonitrile. This was achieved by the addition of 3 ⁇ molecular sieves (EM Science, Gibbstown, NJ) before installation on the machine.
  • DNA ⁇ -cyanoethyl phosphoramidites were purchased from Cruachem (Glasgow, Scotland).
  • the DNA support was 500 ⁇ pore size controlled pore glass (CPG) (PerSeptive Biosystems, Cambridge, MA) derivatized with the appropriate 3' base with a loading of between 30 to 40 mmole per gram.
  • CPG controlled pore glass
  • 2'-OMe RNA ⁇ -cyanoethyl phosphoramidites and CPG supports (500 A) were purchased from Glen Research (Sterling, VA).
  • the DNA phosphoramidites were mixed by the synthesizer according to the manufacturer's protocol (Pharmacia, Uppsala, Sweden).
  • RNA-containing oligonucleotides were synthesized using ethylthiotetrazole (American International Chemical (AIC), Natick, MA) as the activating agent, dissolved to 0.25 M with low water acetonitrile (Aldrich, Milwaukee, WI). Some of the DNA-only syntheses were done using 0.25 M ethylthiotetrazole, but most were done using 0.5 M 1-H-tetrazole (AIC).
  • the thiosulfonating reagent used in all the PS oligonucleotides was 3H-1,2-benzodithiol-3-one 1,1-dioxide (Beaucage Reagent) (R.I. Chemical, Orange, CA, or AIC, Natick, MA) as a 2% solution in low water acetonitrile (w/v).
  • the CPG was air dried and transferred to a 2 ml screw-cap microfuge tube.
  • the oligonucleotide was deprotected and cleaved from the CPG with 2 ml ammonium hydroxide (25-30%).
  • the tube was capped and incubated at room temperature for greater than 20 minutes, then incubated at 55°C for greater than 7 hours.
  • the tubes were removed from the heat block and allowed to cool to room temperature. The caps were removed and the tubes were microcentrifuged at 10,000 rpm for 30 minutes to remove most of the ammonium hydroxide.
  • the liquid was then transferred to a new 2 ml screw cap microcentrifuge tube and lyophilized on a Savant speed vac (Savant, Farmingdale, NY). After drying, the residue was dissolved in 400 ⁇ l of 0.3 M NaCl and the DNA was precipitated with 1.6 ml of absolute EtOH. The DNA was pelleted by centrifugation at 14,000 rpm for 15 minutes, the supernatant decanted, and the pellet dried. The DNA was precipitated again from 0.1 M NaCl as described above. The final pellet was dissolved in 500 ⁇ l H 2 O and centrifuged at 14,000 rpm for 10 minutes to remove any solid material.
  • the supernatant was transferred to another microcentrifuge tube and the amount of DNA was determined spectrophotometrically. The concentration was determined by the optical density at 260 nM.
  • the E 260 for the DNA portion of the oligonucleotide was calculated by using OLIGSOL (Lautenberger (1991) Biotechniques 10:778-780).
  • the E 260 of the 2'-OMe portion was calculated by using OLIGO 4.0 Primer Extension Software (NBI, Plymouth, MN).
  • Oligonucleotide purity was checked by polyacrylamide gel electrophoresis (PAGE) and UV shadowing.
  • 0.2 OD 260 units were loaded with 95% formamide/H 2 O and Orange G dye onto a 20% denaturing polyacrylamide gel (20 cm x 20 cm). The gel was run until the Orange G dye was within one inch of the bottom of the gel. The band was visualized by shadowing with shortwave UV light on a Keiselgel 60 F254 thin layer chromatography plate (EM Separations, Gibbstown, NJ).
  • Standard phosphoramidite chemistry was applied in the synthesis of oligonucleotides containing methylphosphonate linkages using two Pharmacia Gene Assembler Special DNA synthesizers.
  • One synthesizer was used for the synthesis of phosphorothioate portions of oligonucleotides using ⁇ -cyanoethyl phosphoramidites method discussed above.
  • the other synthesizer was used for introduction of methylphosphonate portions. Reagents and synthesis cycles that had been shown advantageous in methylphosphonate synthesis were applied (Hogrefe et al., in Methods in Molecular Biology, Vol.
  • the work up procedure was based on a published procedure (Hogrefe et al. (1993) Nucleic Acids Research 21:2031-2038).
  • the product was cleaved from the resin by incubation with 1 ml of ethanol/acetonitrile/ammonia hydroxide (45/45/10) for 30 minutes at room temperature.
  • Ethylenediamine (1.0 ml) was then added to the mixture to deprotect at room temperature for 4.5 hours.
  • TEAB triethylammonium bicarbonate
  • the resulting mixture was cooled on ice and neutralized to pH 7 with 6 N HCl in 20/80 acetonitrile/water (4-5 ml), then concentrated to dryness using the Speed Vac concentrater.
  • the resulting solid residue was dissolved in 20 ml of water, and the sample desalted by using a Sep-Pak cartridge. After passing the aqueous solution through the cartridge twice at a rate of 2 ml per minute, the cartridge was washed with 20 ml 0.1 M TEAB and the product eluted with 4 ml 50% acetonitrile in 0.1 M TEAB at 2 ml per minute. The eluate was evaporated to dryness by Speed Vac.
  • the crude product was purified by the PAGE procedure, desalted using a Sep-Pak cartridge, then exchanged counter ion into sodium by ethanol precipitation of NaCl solutions, as described above.
  • the product was dissolved in 400 ml water and quantified by UV absorbance at 260 nM.
  • the oligonucleotide constructs which were used are shown schematically in FIG. 9.
  • the HCV-luciferase fusion protein (HCVLUC) contained bases 52 to 338 of HCV sequence.
  • HCV sequences 52-337 (Kato et al. (1990) Proc. Natl. Acad. Sci. (USA) 87:9524) were subcloned from plasmid pHO3-65 (Hoffmann-La Roche, Basel, Switzerland) using PCR.
  • the 5' primer was a T7 primer which is upstream of the HCV region in pHO3-65.
  • the 3' PCR primer contained bases complementary to luciferase and 18 bases complementary to HCV.
  • PCR product was subcloned into pCRII (Invitrogen, San Diego, CA). The correct sequence confirmed and then cloned into pGEMluc (Promega, Madison, WI). This fused HCV sequences to luciferase, substituting the first 9 bases of HCV for the first 6 bases of luciferase to make pGEMHCVLUC. HCVLUC sequences were subcloned into pcDNAIneo (Invitrogen, San Diego, CA) to produce pcHCVLUCneo for stable expression in mammalian cells.
  • HCV sequences 52-337 and 254-1417 (Kato et al. (1990) Proc. Natl. Acad. Sci. (USA) 87:9524) from pHO3-65 and pHO3-62 (Hoffmann-La Roche, Basel, Switzerland), respectively, were subcloned together into pBluescriptIISK (Stratagene, La Jolla, CA) to produce HCV sequences 52-1417 in a single vector. HCV52-1417 was then subcloned into pcDNAIneo (Invitrogen, San Diego, CA) to produce pcHCVneo.
  • pBluescriptIISK Stratagene, La Jolla, CA
  • the pcHCVneo plasmid (10 ⁇ g) was linearized with Xbal restriction enzyme (New England Biolabs, Beverly, MA, 20 U) for 2 hours at 37°C, treated with proteinase K (Stratagene, La Jolla, CA) (0.1 ⁇ g/ ⁇ l) for 1 hour at 37°C and twice phenol/chloroform extracted.
  • the linearized plasmid was ethanol precipitated and isolated from the supernatant by centrifugation.
  • the dried pellet was dissolved in diethylpyrocarbonate (DRPC) (Aldrich, Milwaukee, WI)-treated water to a concentration of 0.5 ⁇ g/ ⁇ l.
  • DRPC diethylpyrocarbonate
  • HCV mRNA was transcribed in vitro using either the Stratagene mRNA Transcription Kit (La Jolla, CA) or the Ambion MEGAscript In vitro Transcription Kit (Austin, TX), and each manufacturers T7 RNA polymerase supplied with each kit. Transcription was performed in the presence of 7.5 mM CTP, 7.5 mM ATP, 75 mM UTP, 6 mM GTP, and 6 mM guanosine hydrate. The reduced GTP concentration allowed the initiation of a high percentage of the transcripts with guanosine to facilitate end-labelling of the mRNA without pretreatment with alkaline phosphatase.
  • the reaction was treated with RNase-free DNase (Stratagene, La Jolla, CA or Ambion, Austin, TX), twice phenol/chloroform extracted, and chromatographed through a G-50 Sephadex spin-column (Boehringer-Mannheim, Indianapolis, IN or Pharmacia, Uppsala, Sweden) to remove unreacted nucleotides and nucleoside.
  • RNase-free DNase (Stratagene, La Jolla, CA or Ambion, Austin, TX)
  • chromatographed through a G-50 Sephadex spin-column (Boehringer-Mannheim, Indianapolis, IN or Pharmacia, Uppsala, Sweden) to remove unreacted nucleotides and nucleoside.
  • the recovered mRNA was quantitated by measuring the UV absorbance at 260 nm using an extinction coefficient of 10000 M -1 cm -1 base -1 of the mRNA.
  • Yields were generally 200-250 ⁇ g RNA/ ⁇ g DNA from a 20 ⁇ l reaction.
  • the mRNA was aliquotted (15 ⁇ g) and stored at -80°C until needed.
  • the mRNA (15 ⁇ g) was end-labelled with 20-25 units of T4 polynucleotide kinase (Pharmacia, Uppsala, Sweden) and 50 ⁇ Ci [ ⁇ - 32 P]ATP (Amersham, Arlington Heights, IL), 6000 Ci/mmol).
  • the labelled mRNA was purified by chromatography through a G-50 Sephadex spin column (Boehringer-Mannheim, Indianapolis, IN, or Pharmacia, Uppsala, Sweden).
  • RNA (20-100 nM) was incubated with a 20 base random DNA library (50-100 ⁇ M) (synthesized on Pharmacia Gene Assembler; all oligonucleotide synthesis, above), boiled previously to dissociate any aggregates, for 90 min at 37°C in 9 ⁇ l 1x buffer (40 mM Tris-HCl pH 7.4, 4 mM MgCl 2 , 1 mM DTT). RNase H (Boehringer-Mannheim, Indianapolis, IN) (1 ⁇ l, 1 unit/ ⁇ l) was then added.
  • the reaction was incubated at 37°C for 10 min, quenched by addition of 10 ⁇ l 90% formamide containing 0.1% phenol red/0.1% xylene cyanol, and frozen on dry ice.
  • the quenched reactions were boiled for 2.5 to 3 minutes, quenched on ice, and 5 to 7 ⁇ l loaded onto a denaturing 4% polyacrylamide gel prerun to 50 to 55°C.
  • the phenol red was typically run to the bottom of the gel, which was then dried at 80°C under vacuum.
  • the gel was autoradiographed using XOMAT film (Kodak, Rochester, NY) or analyzed using phosphorimage technology on a Molecular Dynamics (Sunnyvale, CA) or Bio Rad Phosphorimager (Hercules, CA).
  • Counts were determined by drawing a box around the band of interest and subtracting the background determined with a box drawn nearby. Counts in a product band were compared to total counts in the lane above that band to determine % cleavage. This accounts for the cleavage of small amounts of incomplete transcripts.
  • oligonucleotides 100 ⁇ M in H 2 O were boiled for 1 min to dissociate any aggregates formed between complementary sequences in the mix and 1 ⁇ l (final concentration 10 ⁇ M) was added to 8 ⁇ l 1x RNase H buffer (40 mM Tris-HCl pH 7.4, 4 mM MgCl 2 , 1 mM DTT) containing labelled mRNA (20-100 nM). After a 15 minute preincubation at 37°C, RNase H was added (1 U) and incubated for 10 min at 37°C. The reactions were quenched and analyzed as described above. Sites of cleavage were estimated using DNA and/or RNA molecular size markers.
  • HepG2 cells (ATCC HB8065, American Type Culture Collection, Rockville, MD) were maintained in DMEM with 10% fetal calf serum. Cells were transfected with pcHCVLUCneo by the calcium phosphate procedure (Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual (2nd ed.), Cold Spring Harbor Laboratory Press, pp. 16.30-16.40). Stably transfected clones were selected with (0.75 ⁇ g/ml) Geneticin (Gibco/BRL, Gaithersburg, MD). Clones were evaluated for luciferase expression as described below. A similar luciferase construct lacking HCV sequence was also expressed stably in HepG2 cells.
  • lysis buffer Analytical Luminescence Laboratory, San Diego, CA
  • Cell lysate (20 ⁇ l) was transferred to a White Microlite Plate (Dynatech Laboratories, Chantilly, VA) and 50 ⁇ l substrate A (Analytical Luminescence Laboratory, San Diego, CA) was added to the plate.
  • Luciferase activity was measured in a Microplate Luminometer LB96P (EG&G Berthold, Nashua, NH) by injecting 50 ⁇ l Substrate B (Analytical Luminescence Laboratory, San Diego, CA)), waiting 2 seconds, and then integrating the luminescence signal over 10 seconds.
  • HepG2 HCVLUC cells were seeded onto a 96 well plate (5000 cells/well), and incubated overnight at 37°C. Oligonucleotides were diluted in Optimem (Gibco/BRL, Gaithersburg, MD) containing 10 ⁇ g/ml Lipofectin (Gibco/BRL, Gaithersburg, MD). Medium was removed from cells and replaced with 100 ⁇ l oligonucleotide in Optimem/Lipofectin. Cells were incubated overnight, washed twice with PBS, and then luciferase expression was evaluated.
  • oligonucleotides were mixed with 4ug/ml Cellfectin (Gibco-BRL). Inhibition was measured at four oligonucleotide concentrations, relative to cells treated only with Cellfectin. EC 50 was determined from graphs of the dose response curves. Most active compounds contained 5x5 and 6x6 2'OMe. When more than 12 2'OMe residues were present, oligonucleotides were less active. In this assay, when 18 or 20 2'OMe residues were present (9x) or all 2'OMe) HCVLUC was not inhibitied at any concentration tested (up to 1 uM).
  • oligonucleotide-treated samples were measured in triplicate wells. Untreated control samples were measured in 12 wells. Data was evaluated as % control (treated sample/untreated sample x 100) for each oligonucleotide.
  • HCV C protein coding sequence was selected by Western blot using a rabbit polyclonal antiserum specific for HCV protein (Hoffmann-La Roche, Basel, Switzerland). Cells also expressed HCV RNA as detected by ribonuclease protection assay using probes specific for the 5' UTR and HCV C protein coding sequence.
  • HCV specific riboprobes were prepared which included HCV sequences 52 to 338 (probe 1) or 238 to 674 (probe 2).
  • HepG2 HCV cells (1 x 10 6 cells) were seeded into 100 mm dishes, incubated overnight, then treated with oligonucleotide in the presence of 10 ⁇ g/ml Lipofectin for 4 hours as described above. Cells were incubated overnight. Total RNA was isolated using Trizol (Gibco/BRL, Gaithersburg, MD) according to the manufacturer's instructions.
  • RNA protection assays were performed using 10 ⁇ g of RNA. RNA was hybridized with radiolabelled probe overnight and then digested with single-strand specific RNases A and T1 (RPAII kit, Ambion, Austin, TX) according to the manufacturer's instructions. Ribonuclease digestion products were separated on a 6% polyacrylamide/urea gel. The gel was dried and exposed to x-ray film overnight. Molecular weights were estimated by comparison to RNA standards electrophoresed on the same gel (Ambion, Austin, TX). In addition, amounts of RNA were quantitated on a phosphorimager (BioRad GS250, Hercules, CA).
  • HCV bases 1-2545 were used to generate a recombinant virus with Semliki Forest virus (SFV/HCV) (Gibco/BRL, Gaithersburg, MD). HCV sequences were subcloned from vv1-2545 (Hoffmann-La Roche, Basel, Switzerland) into pSFV1. SFV/HCV sequences were transcribed in vitro using SP6 RNA polymerase. RNA was also transcribed from pSFV2-Helper (Gibco/BRL, Gaithersburg, MD) which provided SFV structural proteins to the recombinant virus. The two RNAs were co-transfected into BHK21 cells (ATCC Ac. No.
  • SFV/HCV Semliki Forest virus
  • pSFV2-Helper produces a structural protein (p62) containing an eight base mutation, converting three arginines to non-basic amino acids. This modification renders the recombinant virus non-infectious unless the p62 protein is first digested with chymotrypsin (Gibco/BRL, Gaithersburg, MD). Recombinant virus required chymotrypsin activation before infection.
  • HepG2 cells (10 5 cells/well in a 6 well dish) were pretreated for 4 hours with different concentrations of oligonucleotide in the presence of 10 ⁇ g/ml Lipofectin in Optimem. Oligonucleotide was then removed, and cells were infected with chymotrypsin activated SFV/HCV (diluted 1/100 in PBS with Ca 2+ , Mg 2+ ) for 1 hour at 37°C. The inoculum was removed, oligonucleotide in Optimum was added to cells, and cells were incubated overnight at 37°C. Cells were then lysed, protein was quantitated and equal amounts of protein were electrophoresed on an SDS/polyacrylamide gel. Protein was detected by Western blotting. The blots were scanned with a flat bed scanner (Umax Data Systems Inc., Hsinchu, Taiwan, ROC) and quantitated with densitometric software (Scan Analysis Biosoft, Ferguson, MO).
  • SFV/HCV virus stocks were prepared as described previously. SFV/HCV inhibition was measured as described previously except that, in some experiments, HepG2 cells were infected with SFV/HCV virus for one hour at 37°C, virus incolum was removed, and then oligonucleotide was added in the presence of lipofectin. In some experiments, cells were not incubated in the presence of oligonucleotide before infection. That oligonucleotides of the invention inhibited HCV C protein production in this assay system is shown below in Table 8. Sequence SEQ ID No.
  • HCV1 Backbone ⁇ 40% Inhibition at 2, 0.4 ⁇ M HCV1 28 PS yes HCV3 35 PS yes HCV1 (EG4-20) 28 0x5 2'OMe PS yes HCV1 (EG4-23) 28 5x5 2'OMe PS yes HCV1 28 6x6 2'OMe PS yes HCV1 28 3x11 2'OMe PS yes HCV1 (EG4-29) 28 0x5 2'OMe PS yes HCV8 9 PS yes HCV28 30 PS yes HCV45 23 PS yes

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Claims (30)

  1. Ein synthetisches Oligonukleotid, umfassend eine Sequenz; die komplementär zu einer Sequenz ist, die aus zwei nicht-zusammenhängenden Bereichen einer Messengeroder genomischen RNA von HCV besteht.
  2. Ein synthetisches Oligonukleotid, umfassend eine Sequenz, die komplementär zu einer Sequenz ist, die aus drei nicht-zusammenhängenden Bereichen einer Messengeroder genomischen RNA von HCV besteht.
  3. Ein synthetisches Oligonukleotid gemäß Anspruch 1 oder 2, wobei einer der nicht-zusammenhängenden Bereiche der 5'-untranslatierte Bereich ist.
  4. Ein Oligonukleotid gemäß Anspruch 1 mit 18 bis 24 Nukleotiden.
  5. Ein Oligonukleotid gemäß Anspruch 1 oder 2, wobei ein Teil des Oligonukleotids die Sequenz GGGGUCCUGGAG (SEQ ID NO:47) oder die Sequenz CAACACUACUCG besitzt.
  6. Ein synthetisches Oligonukleotid gemäß einem der Ansprüche 1-5, das modifiziert ist.
  7. Ein Oligonukleotid gemäß Anspruch 6, wobei die Modifikation wenigstens eine Intemukleotidbindung umfasst, ausgewählt aus der Gruppe bestehend aus Alkylphosphonat, Phosphorthioat, Phosphordithioat, Alkylphosphonothioat, Phosphoramidat, Carbamat, Carbonat, Phosphat-Triester, Acetamidat, Carboxymethylester und Kombinationen davon.
  8. Ein Oligonukleotid gemäß Anspruch 7, umfassend wenigstens eine Phosphorthioat-Intemukleotidbindung.
  9. Ein Oligonukleotid gemäß Anspruch 7, wobei die Intemukleotidbindungen in dem Oligonukleotid Phosphorthioat-lntemukleotidbindungen sind.
  10. Ein Oligonukleotid gemäß Anspruch 6, das wenigstens ein Desoxyribonukleotid umfasst.
  11. Ein Oligonukleotid gemäß Anspruch 6, das wenigstens ein Ribonukleotid umfasst.
  12. Ein Oligonukleotid gemäß Anspruch 10, das zusätzlich wenigstens ein Ribonukleotid umfasst.
  13. Ein Oligonukleotid gemäß Anspruch 12, wobei zwischen zwei Oligoribonukleotid-Bereiche oder der umgekehrten Konfiguration davon ein Oligodesoxyribonukleotid-Bereich zwischengeschaltet ist.
  14. Ein Oligonukleotid gemäß einem der Ansprüche 11-13, wobei das Ribonukleotid ein 2'-O-methyl-Ribonukleotid ist.
  15. Ein Oligonukleotid gemäß Anspruch 12, umfassend wenigstens ein 2'-O-methyl-Ribonukleotid am 3'-Ende des Oligonukleotids.
  16. Ein Oligonukleotid gemäß Anspruch 15, umfassend weiterhin wenigstens ein 2'-O-methyl-Ribonukleotid am 5'-Ende des Oligonukleotids.
  17. Ein Oligonukleotid gemäß Anspruch 1 oder 2, umfassend eine Sequenz ausgewählt aus der Gruppe bestehend aus SEQ ID NO: 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66 und 67, wie in Tabelle 2 dargestellt.
  18. Ein Oligonukleotid gemäß Anspruch 1 oder 2, umfassend eine Sequenz ausgewählt aus der Gruppe bestehend aus SEQ ID NO: 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146 und 147, wie in Tabelle 1C dargestellt.
  19. Ein Oligonukleotid gemäß Anspruch 1 oder 2, umfassend eine Sequenz ausgewählt aus der Gruppe bestehend aus SEQ ID NO: 148, 149, 150, 151, 152, 153, 154, 155, 156, 157 und 158, wie in Tabelle 1D dargestellt.
  20. Ein Oligonukleotid gemäß Anspruch 6, wobei das Oligonukleotid durch eine Schleife selbst-stabilisiert ist.
  21. Ein Oligonukleotid gemäß Anspruch 6, wobei die Modifikation ausgewählt ist aus der Gruppe bestehend aus einer gekerbten Hantel ("nicked dumbbell"), einer geschlossenen Hantel ("closed dumbbell"), 2'-, 3-' und/oder 5'-Caps, Additionen an das Molekül an der Intemukleotid-Phosphatbindung, Oxidation, Oxidation/Reduktion, und Oxidation/reduktive Aminierung, einschließlich Kombinationen davon.
  22. Ein Oligonukleotid gemäß Anspruch 6, wobei wenigstens ein Nukleosid durch Inosin substituiert ist oder wobei wenigstens ein Desoxycytosin durch 5-methyl-Desoxycytosin substituiert ist.
  23. Ein Oligonukleotid gemäß Anspruch 6, wobei das Oligonukleotid durch Einbau von wenigstens einem Triplex-bildenden Strang modifiziert ist.
  24. Ein Oligonukleotid gemäß Anspruch 23 mit einer Nukleotidsequenz ausgewählt aus der Gruppe bestehend aus SEQ ID NO: 166, 167, 168, 169 und 170, wie in Tabelle 1E dargestellt.
  25. Eine pharmazeutische Zusammensetzung, umfassend wenigstens ein Oligonukleotid gemäß einem der Ansprüche 1-24 und einen pharmazeutisch verträglichen Träger.
  26. Eine pharmazeutische Zusammensetzung, umfassend wenigstens zwei verschiedene Oligonukleotide gemäß einem der Ansprüche 1-24.
  27. Ein Oligonukleotid gemäß einem der Ansprüche 1-24 zur Verwendung als eine therapeutisch aktive Verbindung, insbesondere zur Verwendung bei der Kontrolle oder Prävention der Hepatitis C Virus-Infektion oder -Replikation.
  28. Verwendung eines Oligonukleotids gemäß einem der Ansprüche 1-24 zur Zubereitung einer pharmazeutischen Zusammensetzung zur Hemmung der Replikation von Hepatitis Virus C in einer Zelle oder zur Behandlung von Infektion mit Hepatitis Virus C.
  29. Ein Verfahren zum Nachweis von HCV in einer Probe, umfassend die Schritte:
    (a) In-Kontakt-bringen der Probe mit einem synthetischen Oligonukleotid gemäß Anspruch 1, und
    (b) Nachweisen der Hybridisierung des Oligonukleotids an die Nukleinsäure.
  30. Ein Kit zum Nachweis von HCV in einer Probe, umfassend:
    (a) ein synthetisches Oligonukleotid gemäß Anspruch 1; und
    (b) Mittel zum Nachweisen des an die Nukleinsäure hybridisierten Oligonukleotids.
EP96920788A 1995-06-06 1996-06-04 Spezifische oligonukleotide fuer hepatitis c-virus Expired - Lifetime EP0833902B1 (de)

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EP1002878A3 (de) * 1998-11-19 2003-11-12 Tosoh Corporation Hepatitis C Viren RNS-bindendes oligo DNS und Verfahren für dessen Herstellung
ES2288883T3 (es) * 1999-12-13 2008-02-01 Bioniche Life Sciences Inc. Oligonucleotidos sinteticos utiles terapeuticamente.
SK287689B6 (sk) * 2000-06-08 2011-06-06 Intercell Ag Použitie molekuly oligodeoxynukleovej kyseliny na výrobu imunostimulačnej farmaceutickej kompozície a farmaceutický prípravok
US6586584B2 (en) 2001-01-29 2003-07-01 Becton, Dickinson And Company Sequences and methods for detection of Hepatitis C virus
WO2003018747A2 (en) * 2001-08-22 2003-03-06 Isis Pharmaceuticals, Inc. Molecular interaction sites of hepatitis c virus rna and methods of modulating the same
ES2270656B1 (es) * 2004-03-25 2008-03-16 Consejo Sup. Investig. Cientificas Secuencia de rna, construccion de rna y dna, y composicion farmaceutica inhibidoras de la proliferacion del virus causante de la hepatitis tipo c (vhc), y sus aplicaciones.
FR2884522A1 (fr) * 2005-04-19 2006-10-20 Larissa Balakireva Methode d'inhibition de la traduction et/ou la replication d'une sequence d'arn par multimerisation d'une de ses regions d'arn non codant replie

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ATE310817T1 (de) * 1992-09-28 2005-12-15 Chiron Corp Verfahren und zusammensetzungen zur kontrolle der übersetzung der hcv-proteine
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ATE240392T1 (de) 2003-05-15
EP1331267A3 (de) 2003-12-03
ZA964446B (en) 1996-12-06
AU6221996A (en) 1996-12-24
WO1996039500A3 (en) 1997-03-13
DE69628167D1 (de) 2003-06-18
AR002757A1 (es) 1998-04-29
EP1331267A2 (de) 2003-07-30
PT833902E (pt) 2003-09-30

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